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D. Eisenberg, R. Luthy and J. U. Bowie, “VERIFY3D: Assessment of Protein Models with Three-Dimensional Profiles,” Methods in Enzymology, Vol. 277, 1997, pp. 396-404. doi:10.1016/S0076-6879(97)77022-8

has been cited by the following article:

• TITLE: Structural Characterization of the D-Tyr-tRNATyr Deacylase from Bacillus lichenformis, an Organism of Great Industrial Importance

  AUTHORS: Angshuman Bagchi

  KEYWORDS: Molecular Modeling, Molecular Docking, Molecular Dynamics, Industrially Important Microorganism, Ester Hydrolysis, D-Tyr-tRNA Deacylase

  JOURNAL NAME: Computational Molecular Bioscience, Vol.1 No.1, December 28, 2011

  ABSTRACT: A new class of enzyme was established that hydrolyze the ester bond between D-Tyr bound onto its cognate t-RNA. The enzyme is called D-Tyr-tRNA deacylase. The three dimensional structure of the D-Tyr-tRNA deacylase from industrially important microorganism Bacillus lichenformis DSM13 was predicted by comparative modeling approach. Since the protein acts as a dimer a dimeric model of the enzyme was constructed. The interactions responsible for dimerization were also predicted. With the help of docking and molecular dynamics simulations the favourable binding mode of the enzyme was predicted. The probable biochemical mechanism of the hydrolysis process was elucidated. This study provides a rational framework to interpret the molecular mechanistic details of the removal of toxic D-Tyr-tRNA from the cells of industrially important microorganism Bacillus lichenformis DSM13 using the enzyme D-Tyr-tRNA deacylase.